Principal Stan Teitel posted a message on the school's website announcing that he'll retire on Sept. 1 after 13 years at the elite school.
The resignation comes just weeks after 70 students at the high-pressure school were forced to retake Regents exams after they were discovered cheating. Students have said cheating is rampant at the school, in part because of lax enforcement by school officials.
A survey earlier this year in the school's student-run newspaper found that 72 percent of surveyed students had copied another student's homework, and 90 percent of seniors had heard about test questions from other students before taking an exam.
Teitel said in his farewell message that he's leaving to devote more time to his family and to pursue "personal endeavors."
"Thank you to the Stuyvesant community for all of the satisfaction you have afforded me for the last twenty-nine years," wrote Teitel. "It was a genuine pleasure to have served you."
Department of Education officials said Teitel submitted his resignation to Schools Chancellor Dennis Walcott at 3:30 p.m. Friday. A replacement will be named next week, the DOE said in a statement.